monarch-initiative/owlsim-v3

Added tests and documentation for conditional probability index

Fixed CP

Fixed CP calculation

First attempt at a crude bayesian net approach, currently only two …

states are modeled: on and unknown.

Logging, docs and tests

Added additional inline docs

Making makefile top level target for relevant files. …

Note that this is not a robust perf test framework as ontologies/data
may be subject to change - see issue #9

Subsetter (random) for attribute sets, plus tests

Simulated data class using IC for threshold, plus tests.

catching nulls in attSet

New simulated data class - mapping to superclasses; plus tests.

Create data from individuals by mapping single classes to parents, plus …

tests.

minor refactoring

Create derived data by removing whole categories (or the …

reversecomplement for controls), with tests.

Adds timing and cache to match resource

Uses new exceptions

Adds negated IDs and exceptions specific to application state (#6)

Switches to NegationAwareProfileMatcher

Switches to URL validator

Adds negated profile query with IDs to factory

Updates documentation

Adds validation

Adds initial matching resource implementation

Cleans up label mapper

Adds short name string methods for mapping matchers

Adds injection points for integrating with services

Merges @nlwashington changes from before multimodule work

Adds injection for resources

Adds initial KB module

Adds @Inject

Adds initial non-functional dropwizard shell for #6

Updates dependency hierarchy (#6)

Refactors to multi-maven project before adding REST services for #6

Adds constant seed to random for consistent tests

All ICDistro tests use Random(1) for consistency.